90 lines
3.4 KiB
Plaintext
90 lines
3.4 KiB
Plaintext
nextflow.enable.dsl=2
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process STAGE_DATA {
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container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
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memory '2 GB'
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script:
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"""
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BASE="/omic/eureka/digital-patients"
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echo "=== Cleaning up old _parts directories ==="
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find \$BASE -name "*_parts" -type d -exec rm -rf {} + 2>/dev/null || true
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echo "Cleanup done"
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echo "=== Current state of PVC ==="
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ls -la \$BASE/ 2>/dev/null || echo "Base dir missing"
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ls -la \$BASE/imputed/ 2>/dev/null || echo "imputed dir empty/missing"
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ls -la \$BASE/healthy/ 2>/dev/null || echo "healthy dir empty/missing"
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ls -la \$BASE/supporting-data/genome/ 2>/dev/null || echo "genome dir empty/missing"
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echo "=== Downloading files from alien server ==="
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apt-get update -qq && apt-get install -y -qq sshpass > /dev/null 2>&1 || true
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# Function to download via sshpass+scp
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download() {
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local remote="\$1"
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local local_path="\$2"
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mkdir -p \$(dirname "\$local_path")
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echo "Downloading: \$remote -> \$local_path"
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sshpass -p 'bl3rg3r5' scp -o StrictHostKeyChecking=no -P 9100 "omic@nucleus.omic.ai:\$remote" "\$local_path"
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ls -lh "\$local_path"
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}
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# Imputed files (schizophrenia)
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if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" ]; then
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download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.both_sexes.tsv.bgz"
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else
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echo "SKIP: F5_SCHIZO both_sexes already present"
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fi
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if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" ]; then
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download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.female.tsv.bgz"
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else
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echo "SKIP: F5_SCHIZO female already present"
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fi
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if [ ! -f "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" ]; then
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download "/mnt/Avatar/imputed/ukbb/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz" "\$BASE/imputed/F5_SCHIZO.gwas.imputed_v3.male.tsv.bgz"
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else
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echo "SKIP: F5_SCHIZO male already present"
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fi
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# Gnomad files
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if [ ! -f "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt" ]; then
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download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.female.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.female.txt"
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else
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echo "SKIP: gnomad female already present"
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fi
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if [ ! -f "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt" ]; then
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download "/mnt/Avatar/digital_patient/gnomad.genomes.v4.1.sites.male.txt" "\$BASE/healthy/gnomad.genomes.v4.1.sites.male.txt"
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else
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echo "SKIP: gnomad male already present"
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fi
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# hg38.fa (3.3GB)
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if [ ! -f "\$BASE/supporting-data/genome/hg38.fa" ]; then
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download "/mnt/Avatar/dd/synthea/supporting-data/genome/hg38.fa" "\$BASE/supporting-data/genome/hg38.fa"
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else
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echo "SKIP: hg38.fa already present"
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fi
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echo "=== Final verification ==="
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echo "Imputed:"
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ls -lh \$BASE/imputed/*.bgz 2>/dev/null || echo " NONE"
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echo "Healthy:"
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ls -lh \$BASE/healthy/*.txt 2>/dev/null || echo " NONE"
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echo "Genome:"
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ls -lh \$BASE/supporting-data/genome/hg38.* 2>/dev/null || echo " NONE"
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echo "Small files:"
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ls -lh \$BASE/MANE* \$BASE/regulon* \$BASE/LM22* \$BASE/ukbb* 2>/dev/null || echo " NONE"
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echo "=== STAGING COMPLETE ==="
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"""
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}
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workflow {
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STAGE_DATA()
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}
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